Starting phenix.real_space_refine on Tue Sep 24 22:22:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idd_35364/09_2024/8idd_35364.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 45 5.16 5 C 5531 2.51 5 N 1556 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1570 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2227 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2257 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1076 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 157} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1576 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 9, 'TRANS': 215} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.74 Number of scatterers: 8768 At special positions: 0 Unit cell: (101.76, 99.64, 201.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 6 15.00 O 1630 8.00 N 1556 7.00 C 5531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2254 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 57.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 75 through 82 removed outlier: 4.358A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.578A pdb=" N VAL B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.553A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.717A pdb=" N GLU B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 175 through 189 removed outlier: 4.052A pdb=" N ASP B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 removed outlier: 4.411A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 206' Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.957A pdb=" N LEU D 7 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 54 removed outlier: 4.187A pdb=" N LEU D 26 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 75 through 81 removed outlier: 3.713A pdb=" N LYS D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 109 removed outlier: 3.678A pdb=" N ALA D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.534A pdb=" N SER D 121 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 122 " --> pdb=" O LYS D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 122' Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.871A pdb=" N MET D 143 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 190 removed outlier: 3.501A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.782A pdb=" N VAL D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.510A pdb=" N ILE D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 247 removed outlier: 4.388A pdb=" N GLU D 223 " --> pdb=" O PRO D 219 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.518A pdb=" N ALA D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 293 removed outlier: 3.970A pdb=" N ILE D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 269 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.513A pdb=" N LEU D 278 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 5 removed outlier: 3.886A pdb=" N PHE C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 6 through 17 removed outlier: 4.102A pdb=" N VAL C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 48 removed outlier: 3.571A pdb=" N ALA C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.904A pdb=" N ARG C 88 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.774A pdb=" N ALA C 102 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.561A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.217A pdb=" N ASP C 140 " --> pdb=" O HIS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 159 through 199 removed outlier: 3.730A pdb=" N LEU C 169 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 removed outlier: 3.728A pdb=" N ILE C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 207 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 246 removed outlier: 3.986A pdb=" N GLN C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 5.280A pdb=" N GLU C 223 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.301A pdb=" N GLN C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.799A pdb=" N ILE C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 289 removed outlier: 4.237A pdb=" N THR C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.599A pdb=" N GLN E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 56' Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.960A pdb=" N LEU E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 110 removed outlier: 3.921A pdb=" N ASP E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA E 102 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.653A pdb=" N ALA E 121 " --> pdb=" O GLY E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.972A pdb=" N ASP E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 186 removed outlier: 3.830A pdb=" N VAL E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 140 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS E 143 " --> pdb=" O ARG E 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET E 145 " --> pdb=" O MET E 141 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 192 through 203 removed outlier: 3.517A pdb=" N VAL E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 97 through 103 removed outlier: 3.665A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.694A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.985A pdb=" N ALA A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.649A pdb=" N ASP A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.652A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.518A pdb=" N ASP B 6 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 60 " --> pdb=" O ASP B 6 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 8 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER B 58 " --> pdb=" O VAL B 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.586A pdb=" N VAL B 33 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 195 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY B 84 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP B 164 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 58 removed outlier: 4.463A pdb=" N ALA D 93 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 62 removed outlier: 7.751A pdb=" N GLN C 59 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 152 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE C 61 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.112A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 6 through 9 removed outlier: 3.738A pdb=" N ASP A 6 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 60 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 8 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 58 " --> pdb=" O VAL A 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.222A pdb=" N VAL A 33 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 84 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP A 164 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 86 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 212 through 213 377 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2438 1.33 - 1.46: 1620 1.46 - 1.58: 4737 1.58 - 1.70: 9 1.70 - 1.82: 84 Bond restraints: 8888 Sorted by residual: bond pdb=" SD MET C 24 " pdb=" CE MET C 24 " ideal model delta sigma weight residual 1.791 1.744 0.047 2.50e-02 1.60e+03 3.52e+00 bond pdb=" CG1 ILE D 25 " pdb=" CD1 ILE D 25 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.74e+00 bond pdb=" CA ILE A 178 " pdb=" C ILE A 178 " ideal model delta sigma weight residual 1.520 1.538 -0.018 1.20e-02 6.94e+03 2.29e+00 bond pdb=" C VAL B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.26e+00 bond pdb=" C THR D 272 " pdb=" N PRO D 273 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.18e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11816 2.90 - 5.79: 226 5.79 - 8.69: 42 8.69 - 11.58: 13 11.58 - 14.48: 1 Bond angle restraints: 12098 Sorted by residual: angle pdb=" N ALA C 142 " pdb=" CA ALA C 142 " pdb=" C ALA C 142 " ideal model delta sigma weight residual 114.56 108.25 6.31 1.27e+00 6.20e-01 2.47e+01 angle pdb=" N ILE C 205 " pdb=" CA ILE C 205 " pdb=" C ILE C 205 " ideal model delta sigma weight residual 113.53 108.70 4.83 9.80e-01 1.04e+00 2.43e+01 angle pdb=" CB MET C 20 " pdb=" CG MET C 20 " pdb=" SD MET C 20 " ideal model delta sigma weight residual 112.70 127.18 -14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" C VAL A 123 " ideal model delta sigma weight residual 113.42 108.15 5.27 1.17e+00 7.31e-01 2.03e+01 angle pdb=" C ASP B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 4999 16.89 - 33.78: 317 33.78 - 50.67: 62 50.67 - 67.57: 14 67.57 - 84.46: 11 Dihedral angle restraints: 5403 sinusoidal: 1938 harmonic: 3465 Sorted by residual: dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N PHE A 90 " pdb=" CA PHE A 90 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N MET C 191 " pdb=" CA MET C 191 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASN D 190 " pdb=" C ASN D 190 " pdb=" N MET D 191 " pdb=" CA MET D 191 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1219 0.070 - 0.141: 233 0.141 - 0.211: 31 0.211 - 0.281: 3 0.281 - 0.352: 1 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB VAL A 108 " pdb=" CA VAL A 108 " pdb=" CG1 VAL A 108 " pdb=" CG2 VAL A 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA THR C 272 " pdb=" N THR C 272 " pdb=" C THR C 272 " pdb=" CB THR C 272 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1484 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 178 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" C ILE A 178 " -0.072 2.00e-02 2.50e+03 pdb=" O ILE A 178 " 0.027 2.00e-02 2.50e+03 pdb=" N MET A 179 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.015 2.00e-02 2.50e+03 1.95e-02 6.64e+00 pdb=" CG PHE A 46 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 63 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C VAL A 63 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 63 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 64 " -0.014 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2657 2.82 - 3.34: 8563 3.34 - 3.86: 14220 3.86 - 4.38: 15927 4.38 - 4.90: 26279 Nonbonded interactions: 67646 Sorted by model distance: nonbonded pdb=" OH TYR D 52 " pdb=" O ASN D 258 " model vdw 2.302 3.040 nonbonded pdb=" O GLU B 31 " pdb=" OG1 THR B 191 " model vdw 2.315 3.040 nonbonded pdb=" O LEU A 159 " pdb=" OG1 THR A 190 " model vdw 2.316 3.040 nonbonded pdb=" O ILE D 268 " pdb=" OG1 THR D 272 " model vdw 2.317 3.040 nonbonded pdb=" ND2 ASN E 85 " pdb=" OG SER E 169 " model vdw 2.323 3.120 ... (remaining 67641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or resid 177 through 225 or resid 301)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 15 or (resid 16 and (name N or name \ CA or name C or name O or name CB )) or resid 17 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or resid 110 through 133 or \ (resid 134 through 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 or (resid 137 and (name N or name CA or name C or name O or name C \ B )) or resid 138 through 152 or (resid 153 through 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 219 or (resid 220 and (nam \ e N or name CA or name C or name O or name CB )) or resid 221 through 291 or (re \ sid 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5)) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 143 or (resid 144 an \ d (name N or name CA or name C or name O or name CB )) or resid 145 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 199 or (resid 200 and (name N or name CA or name C or name O or name \ CB )) or resid 201 through 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8888 Z= 0.270 Angle : 1.017 14.481 12098 Z= 0.523 Chirality : 0.056 0.352 1487 Planarity : 0.005 0.041 1554 Dihedral : 12.747 84.457 3143 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.24 % Allowed : 0.95 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.21), residues: 1189 helix: -2.33 (0.17), residues: 571 sheet: -1.76 (0.65), residues: 71 loop : -1.89 (0.23), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 214 HIS 0.008 0.001 HIS A 197 PHE 0.045 0.002 PHE A 46 TYR 0.018 0.002 TYR C 288 ARG 0.009 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8341 (mmmt) REVERT: D 113 PHE cc_start: 0.8350 (m-80) cc_final: 0.8083 (m-80) REVERT: D 278 LEU cc_start: 0.8465 (pp) cc_final: 0.7930 (mm) REVERT: C 20 MET cc_start: 0.8805 (tpp) cc_final: 0.7479 (tpt) REVERT: C 137 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8783 (mmmt) REVERT: A 138 ASP cc_start: 0.8219 (t70) cc_final: 0.8008 (t70) outliers start: 2 outliers final: 1 residues processed: 164 average time/residue: 0.1815 time to fit residues: 43.2034 Evaluate side-chains 129 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 285 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS E 179 GLN A 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8888 Z= 0.214 Angle : 0.633 9.649 12098 Z= 0.325 Chirality : 0.041 0.132 1487 Planarity : 0.004 0.050 1554 Dihedral : 8.333 73.205 1347 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.30 % Allowed : 11.26 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1189 helix: -0.83 (0.21), residues: 589 sheet: -1.63 (0.64), residues: 71 loop : -1.64 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.001 PHE C 163 TYR 0.008 0.001 TYR C 215 ARG 0.008 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8682 (mmm) cc_final: 0.8156 (mmm) REVERT: D 113 PHE cc_start: 0.8483 (m-80) cc_final: 0.8266 (m-80) REVERT: C 27 THR cc_start: 0.9231 (m) cc_final: 0.9012 (t) REVERT: C 137 LYS cc_start: 0.9116 (mmpt) cc_final: 0.8888 (mmmt) REVERT: C 222 VAL cc_start: 0.9078 (t) cc_final: 0.8870 (p) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.1589 time to fit residues: 33.0039 Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain A residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 0.0050 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.166 Angle : 0.586 9.864 12098 Z= 0.295 Chirality : 0.040 0.132 1487 Planarity : 0.003 0.032 1554 Dihedral : 8.161 73.226 1347 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.54 % Allowed : 14.69 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.24), residues: 1189 helix: -0.28 (0.21), residues: 609 sheet: -1.46 (0.64), residues: 71 loop : -1.50 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.009 0.001 PHE D 35 TYR 0.010 0.001 TYR C 215 ARG 0.004 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.8612 (mmm) cc_final: 0.8206 (mmm) REVERT: D 282 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8777 (tmm) REVERT: C 27 THR cc_start: 0.9227 (m) cc_final: 0.9011 (t) REVERT: C 137 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8946 (mmmt) REVERT: A 47 MET cc_start: 0.9003 (mpp) cc_final: 0.8798 (mpp) REVERT: A 87 PHE cc_start: 0.8717 (m-10) cc_final: 0.8420 (m-10) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.1781 time to fit residues: 35.2770 Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 GLN E 191 GLN A 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8888 Z= 0.229 Angle : 0.601 10.399 12098 Z= 0.307 Chirality : 0.040 0.162 1487 Planarity : 0.003 0.029 1554 Dihedral : 8.040 74.355 1347 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.96 % Allowed : 16.23 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1189 helix: 0.03 (0.22), residues: 619 sheet: -1.47 (0.59), residues: 81 loop : -1.41 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.004 0.001 HIS E 117 PHE 0.009 0.001 PHE C 163 TYR 0.013 0.001 TYR D 52 ARG 0.004 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7775 (m-30) cc_final: 0.7474 (m-30) REVERT: D 144 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7686 (mmtt) REVERT: D 191 MET cc_start: 0.8558 (tpp) cc_final: 0.8312 (tpp) REVERT: C 137 LYS cc_start: 0.9276 (mmpt) cc_final: 0.8977 (mmmt) outliers start: 25 outliers final: 14 residues processed: 128 average time/residue: 0.1560 time to fit residues: 30.1972 Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0010 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8888 Z= 0.264 Angle : 0.630 9.898 12098 Z= 0.323 Chirality : 0.041 0.167 1487 Planarity : 0.003 0.026 1554 Dihedral : 8.058 71.996 1347 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.61 % Allowed : 17.89 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1189 helix: 0.02 (0.22), residues: 614 sheet: -1.67 (0.58), residues: 81 loop : -1.37 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.013 0.001 PHE A 46 TYR 0.015 0.002 TYR D 52 ARG 0.004 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.8860 (pmm) cc_final: 0.8608 (pmm) REVERT: D 191 MET cc_start: 0.8473 (tpp) cc_final: 0.8197 (tpp) REVERT: C 137 LYS cc_start: 0.9271 (mmpt) cc_final: 0.9030 (mmmt) REVERT: C 162 LEU cc_start: 0.8674 (tt) cc_final: 0.8419 (tp) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.1611 time to fit residues: 30.0132 Evaluate side-chains 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8888 Z= 0.199 Angle : 0.608 10.327 12098 Z= 0.307 Chirality : 0.041 0.179 1487 Planarity : 0.003 0.028 1554 Dihedral : 7.830 69.239 1347 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.37 % Allowed : 18.60 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1189 helix: 0.14 (0.22), residues: 627 sheet: -1.76 (0.57), residues: 81 loop : -1.40 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 214 HIS 0.003 0.001 HIS A 197 PHE 0.012 0.001 PHE A 87 TYR 0.013 0.001 TYR D 52 ARG 0.003 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 MET cc_start: 0.8841 (pmm) cc_final: 0.8617 (pmm) REVERT: D 191 MET cc_start: 0.8404 (tpp) cc_final: 0.8177 (tpp) REVERT: C 137 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8992 (mmmt) REVERT: C 162 LEU cc_start: 0.8708 (tt) cc_final: 0.8490 (tp) outliers start: 20 outliers final: 15 residues processed: 125 average time/residue: 0.1569 time to fit residues: 30.2324 Evaluate side-chains 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8888 Z= 0.193 Angle : 0.626 11.194 12098 Z= 0.312 Chirality : 0.041 0.167 1487 Planarity : 0.003 0.029 1554 Dihedral : 7.723 68.977 1347 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.25 % Allowed : 20.02 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1189 helix: 0.18 (0.22), residues: 623 sheet: -1.69 (0.61), residues: 71 loop : -1.35 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 274 HIS 0.002 0.001 HIS A 197 PHE 0.008 0.001 PHE A 154 TYR 0.012 0.001 TYR D 52 ARG 0.002 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 ASP cc_start: 0.7955 (m-30) cc_final: 0.7720 (m-30) REVERT: B 205 MET cc_start: 0.8847 (pmm) cc_final: 0.8625 (pmm) REVERT: C 137 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8993 (mmmt) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.1613 time to fit residues: 30.3250 Evaluate side-chains 127 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 108 optimal weight: 0.0010 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8888 Z= 0.157 Angle : 0.632 11.494 12098 Z= 0.309 Chirality : 0.041 0.153 1487 Planarity : 0.003 0.031 1554 Dihedral : 7.451 68.181 1347 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.78 % Allowed : 20.14 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1189 helix: 0.24 (0.22), residues: 614 sheet: -1.94 (0.75), residues: 51 loop : -1.33 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 214 HIS 0.003 0.001 HIS A 200 PHE 0.027 0.001 PHE A 87 TYR 0.009 0.001 TYR D 52 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: D 53 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8548 (mt) REVERT: D 191 MET cc_start: 0.8347 (tpt) cc_final: 0.7442 (tpt) REVERT: C 137 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8945 (mmmt) REVERT: C 276 LEU cc_start: 0.9344 (mp) cc_final: 0.8871 (pp) outliers start: 15 outliers final: 9 residues processed: 130 average time/residue: 0.1788 time to fit residues: 34.6728 Evaluate side-chains 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8888 Z= 0.230 Angle : 0.694 12.894 12098 Z= 0.344 Chirality : 0.042 0.214 1487 Planarity : 0.003 0.030 1554 Dihedral : 7.437 69.708 1345 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.78 % Allowed : 21.33 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1189 helix: 0.17 (0.22), residues: 624 sheet: -1.65 (0.62), residues: 71 loop : -1.31 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.021 0.001 PHE A 87 TYR 0.012 0.001 TYR C 215 ARG 0.003 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 137 LYS cc_start: 0.9273 (mmpt) cc_final: 0.9040 (mmmt) outliers start: 15 outliers final: 13 residues processed: 116 average time/residue: 0.1555 time to fit residues: 27.4219 Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8888 Z= 0.199 Angle : 0.684 11.821 12098 Z= 0.336 Chirality : 0.042 0.167 1487 Planarity : 0.003 0.030 1554 Dihedral : 7.380 67.894 1345 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.42 % Allowed : 21.80 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1189 helix: 0.13 (0.22), residues: 630 sheet: -1.64 (0.61), residues: 71 loop : -1.32 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 274 HIS 0.003 0.001 HIS C 136 PHE 0.019 0.001 PHE A 87 TYR 0.011 0.001 TYR C 215 ARG 0.003 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2378 Ramachandran restraints generated. 1189 Oldfield, 0 Emsley, 1189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 20 MET cc_start: 0.9024 (tpp) cc_final: 0.8719 (tpp) REVERT: C 137 LYS cc_start: 0.9290 (mmpt) cc_final: 0.9049 (mmmt) outliers start: 12 outliers final: 10 residues processed: 116 average time/residue: 0.1610 time to fit residues: 28.7712 Evaluate side-chains 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.0050 chunk 81 optimal weight: 6.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.050118 restraints weight = 64106.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.051149 restraints weight = 41400.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051873 restraints weight = 29565.806| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8888 Z= 0.180 Angle : 0.678 11.828 12098 Z= 0.332 Chirality : 0.041 0.177 1487 Planarity : 0.003 0.031 1554 Dihedral : 7.289 67.852 1345 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.66 % Allowed : 21.80 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1189 helix: 0.11 (0.21), residues: 641 sheet: -1.58 (0.61), residues: 71 loop : -1.36 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 274 HIS 0.003 0.001 HIS A 197 PHE 0.020 0.001 PHE A 87 TYR 0.010 0.001 TYR D 52 ARG 0.002 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.92 seconds wall clock time: 33 minutes 20.54 seconds (2000.54 seconds total)